Abstract
BackgroundThe genomes of non-heading Chinese cabbage (Brassica rapa ssp. chinensis), heading Chinese cabbage (Brassica rapa ssp. pekinensis) and their close relative Arabidopsis thaliana have provided important resources for studying the evolution and genetic improvement of cruciferous plants. Natural growing conditions present these plants with a variety of physiological challenges for which they have a repertoire of genes that ensure adaptability and normal growth. We investigated the differential expressions of genes that control adaptability and development in plants growing in the natural environment to study underlying mechanisms of their expression.ResultsUsing digital gene expression tag profiling, we constructed an expression profile to identify genes related to important agronomic traits under natural growing conditions. Among three non-heading Chinese cabbage cultivars, we found thousands of genes that exhibited significant differences in expression levels at five developmental stages. Through comparative analysis and previous reports, we identified several candidate genes associated with late flowering, cold tolerance, self-incompatibility, and leaf color. Two genes related to cold tolerance were verified using quantitative real-time PCR.ConclusionsWe identified a large number of genes associated with important agronomic traits of non-heading Chinese cabbage. This analysis will provide a wealth of resources for molecular-assisted breeding of cabbage. The raw data and detailed results of this analysis are available at the website http://nhccdata.njau.edu.cn.
Highlights
The genomes of non-heading Chinese cabbage (Brassica rapa ssp. chinensis), heading Chinese cabbage (Brassica rapa ssp. pekinensis) and their close relative Arabidopsis thaliana have provided important resources for studying the evolution and genetic improvement of cruciferous plants
Early- and late-flowering mutants have been identified in the model plant Arabidopsis, and many key genes controlling flowering have been isolated in other plants, genes that include FLOWERING LOCUS C (FLC), LFY, FT, and SOC1 [6,7,8]
73.61% (12.85 million), 69.73% (12.53 million), and 68.18% (12.12 million) reads from NHCC001, NHCC002, and NHCC004, respectively, could be mapped to non-heading Chinese cabbage genes modeled from the NHCC001 draft genome, and 63.00% (11.00 million), 60.37% (10.84 million), and 57.98% (10.30 million) reads from the respective accessions could be mapped to unique genes (Table 1)
Summary
The genomes of non-heading Chinese cabbage (Brassica rapa ssp. chinensis), heading Chinese cabbage (Brassica rapa ssp. pekinensis) and their close relative Arabidopsis thaliana have provided important resources for studying the evolution and genetic improvement of cruciferous plants. Natural growing conditions present these plants with a variety of physiological challenges for which they have a repertoire of genes that ensure adaptability and normal growth. We investigated the differential expressions of genes that control adaptability and development in plants growing in the natural environment to study underlying mechanisms of their expression. Brassica rapa L. plants have a rich morphological and genetic diversity, comprising many plant subspecies that humans farm on an enormous scale worldwide. Chinensis), with its five varieties, is an excellent model to study the genetics and mechanisms underlying phenotypic diversity. There were few reports about the flowering of the non-heading Chinese cabbage, or the genes that regulate flowering
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